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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Add check for database definition cross references to also be a general cross reference #28523

Open pgaudet opened 2 months ago

pgaudet commented 2 months ago

(to address https://github.com/geneontology/go-ontology/issues/28146#issuecomment-2233348302 requested by @sjm41 )

There are many cases where the definition cross references and the general cross references don't match.

Minimally for

We should have a check that any def xref to these databases should ALSO be an general xref.

Thanks, Pascale

sjm41 commented 2 months ago

Hi @pgaudet

We should have a check that any def xref to these databases should ALSO be an general xref.

Agreed, though I think my https://github.com/geneontology/go-ontology/issues/28146#issuecomment-2233348302 was for a slightly different check - i.e check for terms that have the same MetaCyc/KEGG (or indeed RHEA/EC) definition xref.

But I guess your suggested check will effectively do the same thing - if we ensure that a def xref ALSO appears as a general xref, then any duplicate def xrefs will get flagged up by the existing checks for duplicate general xrefs.

So, all is probably fine!

pgaudet commented 2 months ago

Right, this is what I meant - once all def xrefs are also general xrefs then we only need to check general xrefs for duplications.